Morphogenesis, the process by which cells move through the embryo to form the shapes and structures of the body, is critical for multicellular lif. Its misregulation leads to a wide range of diseases including birth defects, cancer metastasis and improper wound healing. Genetic screens have been crucial for identifying genes involved in these processes, but traditional genetic screens are blind to large categories of genes, such as those that have a partially redundant function with other pathways, as well as pleiotropic genes. Gene expression profiling techniques such as RNA-seq shed light on these blind spots by taking a snapshot of the transcript level of every gene, regardless of whether it is pleiotropic or partially redundant. I hypothesize that there are undiscovered pleiotropic or partially redundant genes, as well as genes simply not yet found by genetic approaches, that are critical to morphogenesis and which will be revealed by RNA-seq. Ever since the description of the invariant cell lineage of C. elegans development, the nematode has been a powerful embryological tool, allowing researchers to predict exactly when and where an event of interest will take place. Phenomena such as neuron specification, apoptosis, polarized cell division, or cell migration can be anticipated with a spatial resolution of a single cell, and a temporal resolution of minutes. But this cell lineage does not directly address how these phenomena are taking place, and what genes are responsible. Single-cell RNA-seq allows us to profile transcripts levels from each of these cells throughout development, to identify genes that correlate with the well-documented phenomena of development. I will perform single-cell RNA-seq on each individual cell of the C. elegans embryo until the 16-cell stage, thereby creating a molecular lineage to complement the known cellular lineage of development. Regulators of morphogenesis have been difficult to identify, in large part due to the often pleiotropic or partialy redundant functions of these genes. I will analyze the transcriptomes of a variety of gastrulating cell types over time leading up to gastrulation. I hypothesize that there are genes whose expression correlates across cell types as each cell type initiates gastrulation, and that these genes have functional roles in regulating morphogenesis. One of the main contributions of this project will be the transcriptional lineage, which will be made available as a resource to cell and developmental biologists. In order to ensure the utility of this resource, I will program an interactive data visualization web tool. This tool will allow the user to query my data by visually describing a spatiotemporal expression pattern of interest, and receiving information about all the genes that match the described pattern. This tool will bridge a communication gap between computational and non-computational biologists. While these data will be relevant to many questions in developmental and cell biology, I will use them to generate hypotheses about the regulation of morphogenesis, which I will then test in the gastrulating nematode.